Protein profile

VK055_1413

bacterial regulatory helix-turn-helix, lysR family protein

Genome: KpATCC43816

Gene: AIK80035.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVC4
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Amino acids 301
Annotations 4
Features 16
PDB binders 6
Druggability 0.933

Overview

Basic information about this protein and its source genome.

Accession
VK055_1413
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80035.1
Status
annotated
Amino acids
301
Structure source
AlphaFold + ColabFold
GO
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GO:0006351 The synthesis of an RNA transcript from a DNA template.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
53.535
DEG E-value
6.34e-108
Localization
Cytoplasmic
ColabFold pLDDT
88.24

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.933
Structure A0A0H3GVC4
Pocket Pocket 1
P2Rank 0.313
Structure A0A0H3GVC4
Pocket Pocket 1
ColabFold model
FPocket 0.338 · Pocket 1
P2Rank 0.242 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 74 / 4744 genomes with a hit
Normalized 0.016

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
90 291 CDD cd08473 PBP2_CrgA_like_4
92 296 Gene3D G3DSA:3.40.190.290 -
2 91 Gene3D G3DSA:1.10.10.10 -
2 91 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
69 89 Coils Coil Coil
1 59 ProSiteProfiles PS50931 LysR-type HTH domain profile.
1 59 InterPro IPR000847 Transcription regulator HTH, LysR
4 295 PANTHER PTHR30537 HTH-TYPE TRANSCRIPTIONAL REGULATOR
89 298 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
1 85 FunFam G3DSA:1.10.10.10:FF:000001 LysR family transcriptional regulator
4 63 Pfam PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
4 63 InterPro IPR000847 Transcription regulator HTH, LysR
3 87 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
3 87 InterPro IPR036390 Winged helix DNA-binding domain superfamily
88 294 Pfam PF03466 LysR substrate binding domain
88 294 InterPro IPR005119 LysR, substrate-binding

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GVC4
AlphaFold — — full sequence — Viewing
ColabFold VK055_1413
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.933

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 3.99 0.159
2 2.11 0.048

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

56 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
AKG
5Y2V
P73862 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
BEZ
2F7A
O68014 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
CCU
3GLB
P07774 142.1 Da LogP 0.27 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)/C=C\C(=O)O
MLI
4IHS
O68014 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
P33
3FD3
A9CJQ0 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)O
RUB
5Z49
Q9F1R2 310.1 Da LogP -2.50 TPSA 191.0 1 viol. ✓ Clean C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.